Utilizing next-generation sequencing to identify prey DNA in western North Atlantic grey seal (Halichoerus grypus) diet

Increasing grey seal (Halichoerus grypus) abundance in coastal New England
is leading to social, political, economic, and ecological controversies.
We studied grey seal feeding habits through next-generation sequencing of
prey DNA using 16S amplicons from seal scat (N = 74) collected from a
breeding colony on Monomoy Island in Massachusetts, U.S. and report
frequency of occurrence and relative read abundance. We also assigned seal
sex to scat samples using a revised PCR assay. In contrast to current
understanding of grey seal diet from hard parts and fatty acid analysis,
we found no significant difference between male and female diet measured
by alpha and beta diversity. Overall, we detected 24 prey groups, 18 of
which resolved to species. Sand lance (Ammodytes spp.) was the most
frequently consumed prey group, with a frequency of occurrence (FO) of
97.3%, consistent with previous studies, but Atlantic menhaden (Brevoortia
tyrannus), the second most frequently consumed species (FO = 60.8%), has
not been documented in U.S. grey seal diet previously. Our results suggest
that a metabarcoding approach to seal food habits can yield important new
ecological insights, but that traditional hard parts analysis does not
underestimate consumption of Atlantic cod (Gadus morhua; FO = 6.7% Gadidae
spp.) and salmon (Salmo salar; FO = 0%), two particularly valuable species
of concern.